[Freesurfer] using Freesurfer with external storage media

Hi, I remeber a discussion here a month or so back about using Freesurfer with USB hard drives. People were having problems because the hard drive changed file names to lower case (i.e. cor instead of COR). The solution posted to the list was a script that would rename all cor files to

[Freesurfer] mgz conversion

Hey Guys, I have been converting dicom files to COR for the past month and all has been working fine. Now I am trying to convert dicom files to mgz format and I am getting an error every time. I type in the same thing I did for the COR conversion, except I replace -ot cor with -ot mgz. The

Re: [Freesurfer] mgz conversion

Hi David, sounds like your version is old enough that it doesn't know about .mgz format. cheers, Bruce On Mon, 15 Aug 2005, David Soscia wrote: Hey Guys, I have been converting dicom files to COR for the past month and all has been working fine. Now I am trying to convert dicom files

Re: [Freesurfer] mgz conversion

need a command-line and what it prints out David Soscia wrote: Hey Guys, I have been converting dicom files to COR for the past month and all has been working fine. Now I am trying to convert dicom files to mgz format and I am getting an error every time. I type in the same thing I did

Re: [Freesurfer] recon-all

why not? It only adds a few minutes. You can add -nofill -notesselate -nosmooth1 -noinflate1 AFTER the -stage3 flag [EMAIL PROTECTED] wrote: Hi, After processing the data in recon-all stage2, I don't want to repeat stage2 in recon-all stage3. Is there any way to do that? Thx, Antao

[Freesurfer] statistical analysys

Dear Free-surfer Users: when comparing cortical thickness measurements between patients and healthy people by the means of independent -tests, would you recommend correcting by Bonferroni method and consider as significant a p-value given by 0.05/82 or going ahead and just forget about the

[Freesurfer] getting data from specific points

Hi. In order to check for outliers, Id like to extract thickness values for all subjects at a couple chosen points (probably into a text file, so I could import it into SPSS). What would be the best way to do this? Thanks, -Aaron- Aaron L. Goldman Post-Bacc IRTA Genes, Cognition

[Freesurfer] Label colours

Hi, Can labels be loaded in different colours in tkmedit? Alexander Fornito M.psych (Clin. Neuro.)/PhD candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne [EMAIL PROTECTED] ___

[Freesurfer] mri_convert

Hello everyone, I'm having trouble running mri_convert on the dicom images coming off our Siemens Allegra 3T head-only scanner. With this command line: mri_convert 5308.dcm /Volumes/Storage/data/freesurfer/subjects/scfr/mri/orig/001.mgz I get this error: unknown file type for

Re: [Freesurfer] Label colours

Can labels be loaded in different colours in tkmedit? No, sorry. The only thing you can do is convert your lables into a volume and load it as a segmentation volume. -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

RE: [Freesurfer] Editing labels

Hi Kevin, Apologies for the delay. The output is below.Is it not assiging enough vertices to the label after it has been saved in tkmedit? tksurfer 127 lh smoothwm surfer: current subjects dir: /data/flanders/work/alex/freesurfer/subjects surfer: not in scripts dir == using cwd for